[gmx-users] Lennard-Jones Wall ( help please ! )

[Mark Abraham]

Hi,

I asked Berk Hess, who has some experience here, and he suggests:

The 1 nm for wall-r-linpot is far too long. That creates a linear, very
weak, attractive (!) wall potential. This should be 0 or much smaller than
the LJ sigma.
But maybe you already tried that. In that case you should energy minimize
(better) before running MD.

Mark

On Wed, Nov 30, 2016 at 1:21 PM Lamm Gro <lammgro at gmail.com> wrote:

> Dear Gromacs users ,
>
> I am new in Gromacs and I joint to mailing list recently .
> unfortunately no one answered my question about lennard-jones wall .
> Can you please help me about that ?
> I want to use two lennard-jones walls at special distance from each other
> at Z direction but I don't know how I can do that by gromacs .
>
> I used
> ...
> pbc                      = xy
> nwall                    = 2
> wall-atomtype      = opls_740 opls_740
> wall-type               = 9-3
> wall-density           = 50 50
> wall-r-linpot            = 1
>
> But I get lost atom error , I think it's because of some atoms that are
> beyond wall !
> Can you please let me know How i can change the wall location in system ?
>
> Thanks in advance .
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